diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2024-01-11 13:34:33 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-01-16 12:44:37 +0100 |
| commit | 65d021a95032bc2dff81c19158fe9eeeb46f89d4 (patch) | |
| tree | d97de735907270666212257661a5edfbf37388ab /gnu/packages/bioinformatics.scm | |
| parent | a8c1d812a030f07dbc22afa12f82539c3152a9e2 (diff) | |
gnu: python-scikit-bio: Update to 0.5.9.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9.
[source]: Add patch.
[arguments]: Disable one test via #:test-flags; adjust 'compatibility phase;
update 'check phase.
[propagated-inputs]: Remove python-cachecontrol, python-lockfile, and
python-scikit-learn; add python-requests.
* gnu/packages/patches/python-scikit-bio-1887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 12 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c05ca19022..462dd54bc9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4732,58 +4732,43 @@ and record oriented data modeling and the Semantic Web.") (define-public python-scikit-bio (package (name "python-scikit-bio") - (version "0.5.7") + (version "0.5.9") (source (origin (method url-fetch) (uri (pypi-uri "scikit-bio" version)) (sha256 (base32 - "1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3")))) + "0429060pkyq1pm19zb2n1la7czh7b633mp4a4h01j8zfigf49q3s")) + (patches (search-patches "python-scikit-bio-1887.patch")))) (build-system pyproject-build-system) (arguments (list + ;; Accuracy problem + #:test-flags '(list "-k" "not test_fisher_alpha") #:phases '(modify-phases %standard-phases - ;; See https://github.com/biocore/scikit-bio/pull/1826 (add-after 'unpack 'compatibility (lambda _ - (substitute* "skbio/sequence/tests/test_sequence.py" - (("def test_concat_strict_many") - "def _do_not_test_concat_strict_many")) - (substitute* "skbio/stats/distance/_mantel.py" - (("from scipy.stats import PearsonRConstantInputWarning") - "from scipy.stats import ConstantInputWarning") - (("from scipy.stats import PearsonRNearConstantInputWarning") - "from scipy.stats import NearConstantInputWarning") - (("from scipy.stats import SpearmanRConstantInputWarning") "") - (("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)") - "warnings.warn(ConstantInputWarning())") - (("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)") - "warnings.warn(NearConstantInputWarning())") - (("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)") - "warnings.warn(ConstantInputWarning())")) - (substitute* "skbio/diversity/alpha/tests/test_base.py" - (("self.assertEqual\\(pielou_e") - "self.assertAlmostEqual(pielou_e")))) + (substitute* "skbio/diversity/__init__.py" + ((", numeric_only=True") "")))) (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. (invoke "python3" "setup.py" "build_ext" "--inplace"))) (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? (invoke "python3" "-m" "skbio.test"))))))) + (lambda* (#:key tests? test-flags #:allow-other-keys) + (when tests? + (apply invoke "python3" "-m" "skbio.test" test-flags))))))) (propagated-inputs - (list python-cachecontrol - python-decorator + (list python-decorator python-h5py python-hdmedians python-ipython - python-lockfile python-matplotlib python-natsort python-numpy python-pandas - python-scikit-learn + python-requests python-scipy)) (native-inputs (list python-coverage python-pytest)) |